[Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!
Karim Mezhoud
kmezhoud at gmail.com
Fri Apr 1 18:27:52 CEST 2016
Hi,
I tried the scenario 1:
git clone https://github.com/Bioconductor-mirror/canceR
cd canceR
bash ../update_remotes.sh
add files/dir in /vignette
pump version in DESCRIPTION
commit -m "fix vignette"
git svn rebase
git svn dcommit --add-author-from
MBP-de-MacBook:canceR Mezhoud$ git svn dcommit --add-author-from
Committing to
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ...
A inst/doc/canceR.pdf
A vignettes/canceR.Rnw
A vignettes/canceR.latex
A vignettes/image/BrstPrstGSEAlm.png
A vignettes/image/BrstPrstGSEAlm1.jpeg
A vignettes/image/BrstPrstGSEAlm2.jpeg
A vignettes/image/BrstPrstGSEAlm3.jpeg
A vignettes/image/BrstPrstGSEAlm4.jpeg
A vignettes/image/Circos.png
A vignettes/image/Coxph.png
A vignettes/image/GSEA-R.png
A vignettes/image/Mutation1.png
A vignettes/image/clinicalDataDialog.png
A vignettes/image/dialogCircos.png
A vignettes/image/gct_cls.png
..............
A vignettes/image/setWorkspace.jpeg
A vignettes/image/stadGSEAlm4.jpeg
A vignettes/image/stadGSEAlm5.jpeg
A vignettes/image/stadGSEAlm6.jpeg
A vignettes/image/stadGSEAlm7.jpeg
A vignettes/image/stadGSEAlm8.jpeg
A vignettes/image/stadGSEAlm9.jpeg
A vignettes/image/stadGSEAlmCNA.png
A vignettes/image/starting.png
A vignettes/image/starting.svg
A vignettes/image/startingWindow.jpeg
A vignettes/image/whichMSigDB.png
A vignettes/image/whichMSigDB1.jpeg
A vignettes/image/whichMSigDB2.jpeg
A vignettes/image/workspace.png
M DESCRIPTION
ERROR from SVN:
A repository hook failed: Commit blocked by pre-commit hook (exit code 1)
with output:
Traceback (most recent call last):
File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 277, in <module>
process_diff(diff)
File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 112, in process_diff
filename = segs0[1]
IndexError: list index out of range
W: e980c09a87a818a1736f38304e18325b7c0362f5 and refs/remotes/git-svn
differ, using rebase:
:100755 100755 d4a308bbf85b4f0ba06ee27af51f1e76804bad2a
6b7df529709f10184b376d69d5ea9f3ae9e1d3fe M DESCRIPTION
:040000 040000 de5dbdd606d8758565afcadbaf04e5821e71b461
870588b10784e8f5169b2f7bf6377985edd3a735 M inst
:040000 040000 056451883aa9ba2af9e19f8dd2a285d412b9ae60
7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a M vignettes
Current branch master is up to date.
ERROR: Not all changes have been committed into SVN, however the committed
ones (if any) seem to be successfully integrated into the working tree.
Please see the above messages for details.
On Fri, Apr 1, 2016 at 4:27 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:
> Just because git tells you to push, doesn't mean you should push! ;)
> In the devel branch, the upstream repository is an svn repository, so
> instead of pushing you want to do
>
> git svn dcommit --add-author-from
>
> I'll take a look at your earlier email later today.
>
> Dan
>
>
> ----- Original Message -----
> > From: "Karim Mezhoud" <kmezhoud at gmail.com>
> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> > Cc: "bioc-devel" <bioc-devel at r-project.org>
> > Sent: Friday, April 1, 2016 5:17:32 AM
> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes
> or their vignettes are not built by R CMD build!
>
> > Hi,
> > What is the meaning of this? Thanks
> >
> > git checkout devel
> >
> > Previous HEAD position was 1fe033d... add /image
> > Switched to branch 'devel'
> > Your branch is ahead of 'bioc/master' by 49 commits.
> > (use "git push" to publish your local commits)
> >
> > git push
> >
> > fatal: The upstream branch of your current branch does not match
> > the name of your current branch. To push to the upstream branch
> > on the remote, use
> >
> > git push bioc HEAD:master
> >
> > To push to the branch of the same name on the remote, use
> >
> > git push HEAD:master
> >
> >
> > ssh: Could not resolve hostname head: nodename nor servname provided, or
> > not known
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> >
> >
> >
> > On Fri, Apr 1, 2016 at 1:09 AM, Karim Mezhoud <kmezhoud at gmail.com>
> wrote:
> >
> >> Hi,
> >> I repeated several times the clone ....And I success for one time the
> >> commit but with mistakes. I can't repeat the steps again.
> >>
> >> git merge master --log
> >>
> >> And I had a conflict between versions. I omit conflicts and I
> >>
> >> git svn dcommit --add-author-from
> >>
> >> ##############################
> >> A....
> >> A.....
> >> A.....
> >> All files are added
> >>
> >>
> >> ERROR from SVN:
> >> A repository hook failed: Commit blocked by pre-commit hook (exit code
> 1)
> >> with output:
> >> Traceback (most recent call last):
> >> File
> >>
> "/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
> >> line 277, in <module>
> >> process_diff(diff)
> >> File
> >>
> "/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
> >> line 112, in process_diff
> >> filename = segs0[1]
> >> IndexError: list index out of range
> >>
> >> W: bc9bed01f7b03d6da5b345d2699822d197b202b4 and
> refs/remotes/git-svn-devel
> >> differ, using rebase:
> >> :100644 100644 d4a2ec80b4623bc866606de39e06ff33e60056a8
> >> cea7fa70e88adf9033fce5d7a846944c3431ee85 M .gitignore
> >> :100755 100755 6b7df529709f10184b376d69d5ea9f3ae9e1d3fe
> >> 15ac213b3484b967cceabc0c0e22bda2d654b27a M DESCRIPTION
> >> :040000 040000 e2c182ee6256b99e4c83e2dac8e7576fedeef302
> >> 7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a M vignettes
> >>
> >> It seems that there is already a rebase-apply directory, and
> >> I wonder if you are in the middle of another rebase. If that is the
> >> case, please try
> >> git rebase (--continue | --abort | --skip)
> >> If that is not the case, please
> >> rm -fr "/Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply"
> >> and run me again. I am stopping in case you still have something
> >> valuable there.
> >> rebase refs/remotes/git-svn-devel: command returned error: 1
> >> @#####################################
> >>
> >>
> >>
> >>
> >> I removed
> >>
> >>
> >> rm -fr /Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply
> >>
> >> and
> >>
> >> git svn rebase
> >>
> >> ###########################
> >> First, rewinding head to replay your work on top of it...
> >> Applying: canceR0.99.1
> >> Using index info to reconstruct a base tree...
> >> .git/rebase-apply/patch:102: trailing whitespace.
> >>
> >> .git/rebase-apply/patch:103: trailing whitespace.
> >>
> >> .git/rebase-apply/patch:106: trailing whitespace.
> >>
> >> .git/rebase-apply/patch:113: trailing whitespace.
> >>
> >> .git/rebase-apply/patch:120: trailing whitespace.
> >>
> >> warning: squelched 7388 whitespace errors
> >> warning: 7393 lines add whitespace errors.
> >> Falling back to patching base and 3-way merge...
> >> error: The following untracked working tree files would be overwritten
> by
> >> merge:
> >> vignettes/._canceR.pdf
> >> Please move or remove them before you can merge.
> >> Aborting
> >> error: Failed to merge in the changes.
> >> Patch failed at 0001 canceR0.99.1
> >> The copy of the patch that failed is found in: .git/rebase-apply/patch
> >>
> >> When you have resolved this problem, run "git rebase --continue".
> >> If you prefer to skip this patch, run "git rebase --skip" instead.
> >> To check out the original branch and stop rebasing, run "git rebase
> >> --abort".
> >>
> >> rebase refs/remotes/git-svn-devel: command returned error: 128
> >> ###############################
> >>
> >> I did not found any whitespace in path file line: 102, 103, 106, 113,
> 120
> >>
> >> patch file from 112 to 120:
> >>
> >> *@@ -0,0 +1,73 @@*
> >>
> >> *+Match_GeneList_MSigDB <- function(){*
> >>
> >> *+ *
> >>
> >> *+ *
> >>
> >> *+ ttdialogMSigDB<-tktoplevel()*
> >>
> >> *+ tktitle(ttdialogMSigDB) <- "Setting MSigDB Directory"*
> >>
> >> *+ *
> >>
> >> *+ fromDir <- function(){*
> >>
> >> *+ ##Select directory which has MSigDB*
> >>
> >> *+ myGlobalEnv$dirMSigDBPath <- tk_choose.dir()*
> >>
> >> *+ tkdestroy(ttdialogMSigDB)*
> >>
> >> *+ #return(dirMSigDBPath)*
> >>
> >> *+ }*
> >>
> >> *+ *
> >>
> >> *+ fromExample <- function(){*
> >>
> >> *+ ##Or select MSigDB from package*
> >>
> >> *+ myGlobalEnv$dirMSigDBPath <-
> >> paste(path.package("canceR"),"/extdata/MSigDB/",sep="")*
> >>
> >> *+ tkdestroy(ttdialogMSigDB)*
> >>
> >> *+ #return(dirMSigDBPath)*
> >>
> >>
> >>
> >> after I git svn rebase
> >>
> >> It seems that there is already a rebase-apply directory, and
> >> I wonder if you are in the middle of another rebase. If that is the
> >> case, please try
> >> git rebase (--continue | --abort | --skip)
> >> If that is not the case, please
> >> rm -fr "/Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply"
> >> and run me again. I am stopping in case you still have something
> >> valuable there.
> >> rebase refs/remotes/git-svn-devel: command returned error: 1
> >>
> >> On Tue, Mar 29, 2016 at 8:12 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
> >> wrote:
> >>
> >>>
> >>>
> >>>
> >>>
> >>> ----- Original Message -----
> >>> > From: "Karim Mezhoud" <kmezhoud at gmail.com>
> >>> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> >>> > Cc: "bioc-devel" <bioc-devel at r-project.org>
> >>> > Sent: Tuesday, March 29, 2016 12:05:03 PM
> >>> > Subject: Re: [Bioc-devel] 49 software packages either have no
> vignettes
> >>> or their vignettes are not built by R CMD build!
> >>>
> >>> > Thank you,
> >>> > I am in devel branch (git checkout devel) .
> >>> >
> >>> > when I "git svn rebase" I get all changed files with message: needs
> >>> update.
> >>>
> >>> This doesn't happen with me:
> >>>
> >>> clone https://github.com/kmezhoud/canceR.git
> >>> cd canceR/
> >>> ../mirror/update_remotes.sh
> >>> git checkout devel
> >>> git svn rebase
> >>>
> >>>
> >>> No error. You might try doing a fresh clone in another directory.
> >>>
> >>> Dan
> >>>
> >>>
> >>>
> >>> > How can I update.
> >>> > km
> >>> >
> >>> >
> >>> >
> >>> >
> >>> > On Tue, Mar 29, 2016 at 4:16 PM, Dan Tenenbaum <
> dtenenba at fredhutch.org>
> >>> > wrote:
> >>> >
> >>> >>
> >>> >>
> >>> >> ----- Original Message -----
> >>> >> > From: "Karim Mezhoud" <kmezhoud at gmail.com>
> >>> >> > To: "bioc-devel" <bioc-devel at r-project.org>
> >>> >> > Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> >>> >> > Sent: Tuesday, March 29, 2016 6:11:15 AM
> >>> >> > Subject: Re: [Bioc-devel] 49 software packages either have no
> >>> vignettes
> >>> >> or their vignettes are not built by R CMD build!
> >>> >>
> >>> >> > Dear Dr Dan,
> >>> >> > Thank you for this note.
> >>> >> > In my case (canceR), I am using sweave and having:
> >>> >> >
> >>> >> > checking PDF version of manual ... [8s/19s] OK
> >>> >> >
> >>> >> > during R CMD Check.
> >>> >> >
> >>> >> > I need to sync devel version using git-mirrors (
> >>> >> > https://www.bioconductor.org/developers/how-to/git-mirrors/).
> >>> >> > I am following scenario 2.
> >>> >> > When I fork bioc-mirror/canceR I get two repo with the same name
> in
> >>> my
> >>> >> > github.
> >>> >> >
> >>> >>
> >>> >> It sounds like you already had a github repository before the fork.
> In
> >>> >> this case, do not fork, just run the update_remotes.sh script.
> >>> >> Dan
> >>> >>
> >>> >>
> >>> >> > at step 4 of tutorial, I can not push some changes:
> >>> >> >
> >>> >> > error: unable to read askpass response from 'rpostback-askpass'
> >>> >> > fatal: could not read Username for 'https://github.com': Device
> not
> >>> >> > configured
> >>> >> >
> >>> >> > 1- How can I configure access to bioc-mirror/canceR.
> >>> >> >
> >>> >> > 2- What is the utility of the fork if we can commit directly to
> >>> >> > bioc-mirror/canceR?
> >>> >> >
> >>> >> > Thank you
> >>> >> > Karim
> >>> >> >
> >>> >> >
> >>> >> > On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum <
> >>> dtenenba at fredhutch.org>
> >>> >> > wrote:
> >>> >> >
> >>> >> >> Attention package maintainers,
> >>> >> >>
> >>> >> >> When building an R package, if R thinks there is a vignette, it
> will
> >>> >> emit
> >>> >> >> this line during R CMD build:
> >>> >> >>
> >>> >> >> * creating vignettes ... OK
> >>> >> >>
> >>> >> >> If there is either no vignette, or in the case of non-sweave
> >>> vignettes,
> >>> >> >> something is not set up correctly (there are many things that
> can go
> >>> >> >> wrong), you won't see that line of output.
> >>> >> >>
> >>> >> >> This means your vignette will not be available on our web site,
> nor
> >>> to
> >>> >> end
> >>> >> >> users who install your package.
> >>> >> >>
> >>> >> >> So going to the build system and looking through all R CMD build
> >>> output
> >>> >> to
> >>> >> >> see which output files do NOT have that line, returns 49 matches:
> >>> >> >>
> >>> >> >> $ grep -L "creating vignettes ..." *.buildsrc-out.txt
> >>> >> >> a4Base.buildsrc-out.txt
> >>> >> >> a4Classif.buildsrc-out.txt
> >>> >> >> a4Core.buildsrc-out.txt
> >>> >> >> a4Preproc.buildsrc-out.txt
> >>> >> >> a4Reporting.buildsrc-out.txt
> >>> >> >> affxparser.buildsrc-out.txt
> >>> >> >> affyio.buildsrc-out.txt
> >>> >> >> AffyTiling.buildsrc-out.txt
> >>> >> >> aroma.light.buildsrc-out.txt
> >>> >> >> arrayQuality.buildsrc-out.txt
> >>> >> >> bigmemoryExtras.buildsrc-out.txt
> >>> >> >> BiocCaseStudies.buildsrc-out.txt
> >>> >> >> BiocGenerics.buildsrc-out.txt
> >>> >> >> BiocInstaller.buildsrc-out.txt
> >>> >> >> BufferedMatrixMethods.buildsrc-out.txt
> >>> >> >> canceR.buildsrc-out.txt
> >>> >> >> CGHbase.buildsrc-out.txt
> >>> >> >> CoCiteStats.buildsrc-out.txt
> >>> >> >> daMA.buildsrc-out.txt
> >>> >> >> dcGSA.buildsrc-out.txt
> >>> >> >> DynDoc.buildsrc-out.txt
> >>> >> >> ExperimentHub.buildsrc-out.txt
> >>> >> >> flipflop.buildsrc-out.txt
> >>> >> >> GraphAT.buildsrc-out.txt
> >>> >> >> HDF5Array.buildsrc-out.txt
> >>> >> >> hypergraph.buildsrc-out.txt
> >>> >> >> Icens.buildsrc-out.txt
> >>> >> >> impute.buildsrc-out.txt
> >>> >> >> mcaGUI.buildsrc-out.txt
> >>> >> >> microRNA.buildsrc-out.txt
> >>> >> >> minet.buildsrc-out.txt
> >>> >> >> MSstats.buildsrc-out.txt
> >>> >> >> multtest.buildsrc-out.txt
> >>> >> >> netresponse.buildsrc-out.txt
> >>> >> >> nondetects.buildsrc-out.txt
> >>> >> >> normalize450K.buildsrc-out.txt
> >>> >> >> oligoClasses.buildsrc-out.txt
> >>> >> >> parglms.buildsrc-out.txt
> >>> >> >> plier.buildsrc-out.txt
> >>> >> >> preprocessCore.buildsrc-out.txt
> >>> >> >> ProtGenerics.buildsrc-out.txt
> >>> >> >> QUALIFIER.buildsrc-out.txt
> >>> >> >> RPA.buildsrc-out.txt
> >>> >> >> scde.buildsrc-out.txt
> >>> >> >> seqplots.buildsrc-out.txt
> >>> >> >> SJava.buildsrc-out.txt
> >>> >> >> spotSegmentation.buildsrc-out.txt
> >>> >> >> stepNorm.buildsrc-out.txt
> >>> >> >> XVector.buildsrc-out.txt
> >>> >> >>
> >>> >> >> Some of these (a4Base, a4Classif and many more) just have no
> >>> vignettes/
> >>> >> >> directory so no vignettes at all.
> >>> >> >>
> >>> >> >>
> >>> >> >> Others (ExperimentHub for example) have an empty vignettes
> >>> directory.
> >>> >> >>
> >>> >> >> But others (QUALIFIER for example) have a vignettes directory
> with
> >>> >> >> vignette files.
> >>> >> >>
> >>> >> >> If any packages you maintain do not have a vignette, please add
> one.
> >>> >> >>
> >>> >> >> If your package has a vignette in the vignettes/ directory but is
> >>> in the
> >>> >> >> above list, then you need to fix it.
> >>> >> >>
> >>> >> >> This page is a good place to start tracking down the problem:
> >>> >> >>
> >>> >> >> http://yihui.name/knitr/demo/vignette/
> >>> >> >>
> >>> >> >> For non-sweave (usually knitr) vignettes, the important things to
> >>> check
> >>> >> >> are:
> >>> >> >>
> >>> >> >> - knitr should be in the Suggests field in DESCRIPTION
> >>> >> >> (if using BiocStyle with rmarkdown, be sure BiocStyle and
> >>> rmarkdown
> >>> >> are
> >>> >> >> also in Suggests).
> >>> >> >> - VignetteBuilder: knitr should be in DESCRIPTION
> >>> >> >> - The actual vignette file should have a %\VignetteEngine line;
> see
> >>> link
> >>> >> >> above
> >>> >> >> for more information.
> >>> >> >>
> >>> >> >> How can you tell if you've fixed the problem?
> >>> >> >> run R CMD build on your package and look for the line
> >>> >> >>
> >>> >> >> * creating vignettes ... OK
> >>> >> >>
> >>> >> >> In the output. If you don't see that line, your vignette has not
> >>> been
> >>> >> >> built.
> >>> >> >>
> >>> >> >> If you've tried all these things and are still running into
> >>> problems,
> >>> >> >> contact bioc-devel.
> >>> >> >>
> >>> >> >> Dan
> >>> >> >>
> >>> >> >> _______________________________________________
> >>> >> >> Bioc-devel at r-project.org mailing list
> >>> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
>
[[alternative HTML version deleted]]
More information about the Bioc-devel
mailing list